gemma.R

Bioc current

A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses

v3.8.0 · software · Apache License (>= 2)

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.16 · Nov 2, 2022

Current · Requires R 4.6

1.0 In 8 of 49 releases 3.23

Description

Low- and high-level wrappers for Gemma's RESTful API. They enable access to curated expression and differential expression data from over 10,000 published studies. Gemma is a web site, database and a set of tools for the meta-analysis, re-use and sharing of genomics data, currently primarily targeted at the analysis of gene expression profiles.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

142 40 exported

Complexity

3.5 avg / 32 max

Call network

142 nodes / 213 edges

Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.

Call graph

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Lowest coverage

Per-function coverage is not measured for this package yet.

Code

Structure

Lines of code

12,772

Files

157

Compiled share

Has compiled src

Language breakdown

R 6,524 (51.1%)Tests 852 (6.7%)Docs 3,973 (31.1%)Vignettes 1,423 (11.1%)

API

Exported functions

Internal functions

102

Recent export changes

v3.22+1 get_dataset_publications

v3.21+2 get_annotation_children, get_annotation_parents −1 get_dataset_design

Testing & CI

Has tests

Yes

Test-to-code ratio

0.13

testthat edition

CI present

Yes

CI type

["github-actions"]

PR gated

Yes

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

Unsafe pattern score

Dep constraint coverage

Secret pattern count

Bundled 3rd-party code

2 items

Portability & License

Min R version

–

System requirements

–

C++ standard

–

License

Apache License (>= 2)

License flags

SPDX valid, OSI approved

History

Versions

First release

2023-01-24

Latest release

2026-04-28

Avg cadence

133 days

Cold removal rate

100%

Dep drift

LOC over versions

Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.

Documentation

READMEYes · 163 wordsVignettesYes · dynamicpkgdown siteYesNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 79%
Return-value docs: 93%
References docs: 1%

Topics

Software

Software › Infrastructure › DataImport

Software › Technology › Microarray

Software › Technology › SingleCell

ThirdPartyClient

Software › BiologicalQuestion › DifferentialExpression

Software › AssayDomain › GeneExpression

Software › StatisticalMethod › Bayesian

Software › WorkflowStep › Annotation

Software › WorkflowStep › ExperimentalDesign

Software › WorkflowStep › Normalization

Software › WorkflowStep › BatchEffect

Software › WorkflowStep › Preprocessing

People

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